SMP Nuts and Bolts

Assess Conditions and Identify Risks

Leah Weaver collecting a benthic macroinvertebrate sample on the Conejos River (Daniel Boyes/Rio Grande Headwaters Restoration Project)

Aquatic biota in riverine systems include microbes, periphyton (attached algae), macrophytes (aquatic plants), macroinvertebrates (aquatic insects), fish, amphibians, and any other organism that is part of the aquatic biological community for all or part of its life history. Ecosystems that can support complex trophic structures (food/energy webs) are generally healthier and more resilient to stressors like human activities, drought, and climate change.

The presence of federally listed aquatic Threatened or Endangered Species, as well as State Species of Concern, should be investigated in the area of interest. Their presence often signals a history of data collection, habitat restoration projects, and water management efforts that can inform an SMP.

The biotic composition of a stream is impacted by all other stream health factors. Because the productivity and survival of aquatic organisms is dependent on all other aspects of stream function, the aquatic biota variable is a prime indicator of overall stream health (Herman and Nejadhashemi 2015).

Analysis of aquatic biota should begin with a comprehensive review of all available data. Decisions regarding assessment level, data collection, method selection, and data analysis should be made based on SMP goals and existing data.

Data Types

Fish species distribution and age class structure

Native fish species range

Trout fishery condition based on population characteristics

Macroinvertebrate community health indices

Total macroinvertebrate biomass

Amphibian presence/absence

Potential Data Sources

Aquatic species surveys conducted by CPW, USFS, BLM, and others and associated reports

CDPHE macroinvertebrate MMI scores

Colorado Natural Heritage Program Rare and Imperiled Animals Datasets

Independent benthic macroinvertebrate sample collection and analysis of individual or combined metrics

Independent fish surveys (electroshocking)

Conversations with local residents

Interviews with regional aquatic biologists

Rapid qualitative assessment of benthic macroinvertebrates during field visits

Tips for Success


Colorado Parks and Wildlife (CPW), U.S. Forest Service (USFS), Bureau of Land Management (BLM), other federal and state agencies, and local watershed groups (Trout Unlimited, local coalitions) often conduct surveys on aquatic species such as macroinvertebrates, fish, and amphibians. Data are typically compiled and analyzed in reports, and survey results and companion reports are available to the public, often at the site or reach scale. Contact local state and federal land management staff to identify existing data sources, and assess the quality and spatial and temporal distribution of these data. In many cases, additional aquatic biota data do not need to be collected.


The Colorado Department of Public Health and Environment (CDPHE) monitors streams throughout Colorado for protection of water quality, and has a standardized methodology for assessing the health of benthic macroinvertebrate communities. Their principal indicator is a Multi-Metric Index (MMI) based on direct benthic macroinvertebrate sample data. By using five to six equally weighted metrics, the MMI combines measures of diversity, abundance, pollution tolerance, community structure, and other factors to generate a normalized score of 0-100 for each sample. Scores may then be compared to reference threshold scores for one of three generalized Colorado biotypes (mountains, transition, plains). This document contains attainment and impairment thresholds by biotype, as well as benthic macroinvertebrate sampling collection and analysis guidelines.


The three most common indicators that are used to assess the health of the benthic community are MMI, Shannon-Wiener Diversity Index (SDI), and Hilsenhoff Biotic Index (HBI). The SDI is a mathematical measure of species diversity within a given community. For benthic macroinvertebrates, values range from 0-5, and higher values indicate higher species diversity (MacArthur 1965). The HBI reveals the relative abundance of pollution-tolerant species. Scores range from 0-10, where a higher value indicates more pollution-tolerant species are present (Hilsenhoff 1987). In “grey” areas where the MMI alone is not sufficient, the SDI and HBI can also be compared to attainment and impairment threshold values.


CDPHE regularly summarizes state-wide data in an Integrated Water Quality Monitoring and Assessment Report (see the most recent report, completed in 2022). The report includes basin summaries, as well as a use attainment table broken out by stream segment.


In general, collection of biological data is relatively inexpensive (low to moderate cost, depending on organism and number of reaches/monitoring locations). So in cases where existing data are limited or data quality is questionable, independent data collection and analysis may be a viable option.


Conducting minimum flow evaluations can provide additional data regarding fishery health by providing information about the minimum flows necessary to sustain healthy populations of resident aquatic biota by season; this type of analysis may also lead to potential opportunities for improving aquatic health.


Crystal River Management Plan

Assessment Level: Level 1

The Crystal River Management Plan relied on existing data sources and discussions with local residents and regional experts to develop their aquatic biota score within the Functional Assessment of Colorado Streams (FACStream) assessment framework.

For the Crystal, conversations with local residents made it clear that the area has long lacked a robust fishery. Expert review of fish species diversity, total biomass, and age class distribution data collected by CPW at multiple points along the river helped assess the degree of departure of the existing fishery from natural conditions. These conclusions were corroborated by a direct comparison of data collected on the Crystal with nearby reference reaches. Macroinvertebrate data collected by USFS and the Roaring Fork Conservancy, following CDPHE protocols, was used to characterize the structure and health of the macroinvertebrate communities.

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Yampa River Health Assessment and Streamflow Management Plan

Assessment Level: Level 2

Similar to the Crystal, the Yampa River Health Assessment and Streamflow Management Plan relied heavily on existing data sources and communications with a regional aquatic biologist, but augmented this information with rapid qualitative assessment of benthic macroinvertebrates during field visits. This information was assimilated by experts into a single score for the Aquatic Biota variable (named “Trophic Structure” in the Yampa River SMP) within the Functional Assessment of Colorado Streams (FACStream) assessment framework.

This variable includes all trophic levels and taxonomic groups (fish, insects, microbes, etc.) and derives one single score for this variable based on all available data. The scores depend on community structure, composition, and diversity, and can range from zero (fundamentally altered community structure dominated by exotic species, lacking several important functional guilds) to 100 (natural community structure appropriate for a well-functioning river in its process domain).

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Rio Grande, Conejos River, and Saguache Creek Stream Management Plans

Assessment Level: Level 3

The Rio Grande Headwaters Restoration Project (RGHRP) is conducting a fisheries and aquatic life assessment, which includes an assessment of benthic macroinvertebrates and fish populations at 25 reaches within their project area. They expect to summarize quantitative results by reach to identify “problem” areas and areas of opportunity.

To assess benthic macroinvertebrate communities, RGHRP reviewed existing data related to macroinvertebrate communities across their watershed, including the USGS water quality data portal, CPW River Watch data, CDPHE data and data compilations, and other relevant studies. After identifying data gaps, particularly on the Conejos River and Saguache Creek, they decided to collect benthic macroinvertebrate community samples at all project reaches to supplement existing data.

RGHRP collected benthic macroinvertebrate samples at 24 monitoring locations using a modified kick-net and following CDPHE’s sampling protocols. They sent their samples to a laboratory for taxonomic determinations, calculated three indicator indices (Multi-Metric Index (MMI), Shannon-Wiener Diversity Index (SDI), and Hilsenhoff Biotic Index (HBI)), and compared site-specific results to the attainment and impairment thresholds set by CDPHE for the appropriate biotype.

To assess fish populations, RGHRP sent the spatial extents of their project reaches to CPW and requested all existing fish population survey data from the last 10 years at those locations. Although data were limited on Saguache Creek, CPW was able to provide existing data for at least one site within every SMP reach extent. The site-specific fish population data consisted of information such as fish species, abundance, and age class distributions.

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